Flexibility of Dicer Studied by Implicit Solvent Molecular Dynamics Simulations

• Autorzy: Sarzyńska J. , Mickiewicz A. , Miłostan M. , Łukasiak P. , Błażewicz J. , Figlerowicz M. , Kuliński T.
• Języki publikacji: EN

Abstrakty

EN

Dicer is an enzyme responsible for processing double-stranded RNAs and plays a key role in an RNAi mechanism. Structural insight into the Dicer is provided by the crystal structure of eukaryotic Dicer from Giardia intestinalis. It has been proposed that the structure has three structurally rigid regions that are connected by the flexible hinges. Flexibility of the Dicer is believed to be a critical feature for its function. Spatial arrangement of the RNA-recognition and the catalytic regions is crucial for producing small RNAs of defined length. It has been suggested that in the Giardia Dicer a Platform domain may help in specific arrangement of these regions. To learn more about the role of the Platform domain in Giardia Dicer, we have performed molecular dynamics (MD) simulations of the whole Dicer (WT Dicer) and the Dicer with a deleted platform domain (delta Plf Dicer). The MD simulations were carried out in an implicit solvent model with two implementations of analytic Generalized Born (GB) solvation model in CHARMM: GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple Switching). To detect the key global motions of the Dicer, a principal component analysis (PCA) of the obtained MD trajectories has been used. To further explore the motion of the Dicer, we performed a domain motion analysis with the DYNDOM program. The simulations show that both WT Dicer and delta Plf Dicer display flexibility which can be described as a movement of two or three domains. The removal of the Platform substantially changed the flexibility and arrangement of these domains. During the MD simulations of delta Plf Dicer an large movement of the RNA-recognition domain was observed.

Słowa kluczowe

EN

implicit solvent model; principal component analysis; molecular dynamics; domain motions; Giardia Dicer

• Wydawca: Institute of Bioorganic Chemistry Scientific Publishers OWN, Polish Academy of Sciences
• Czasopismo: Computational Methods in Science and Technology
• Rocznik: 2010
• Tom: Vol. 16, No. 1
• Strony: 97--104
• Opis fizyczny: Bibliogr. 24 poz., rys.

Twórcy

autor

Sarzyńska J.

autor

Mickiewicz A.

autor

Miłostan M.

autor

Łukasiak P.

autor

Błażewicz J.

autor

Figlerowicz M.

autor

Kuliński T.

• Institute of Bioorganic Chemistry, Polish Academy of Sciences ul. Noskowskiego 12/14, 61-704 Poznań, Poland,

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